Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation

Cell Host Microbe. 2021 Mar 10;29(3):362-377.e11. doi: 10.1016/j.chom.2020.12.008. Epub 2021 Jan 12.


Immunomodulatory drugs can inhibit bacterial growth, yet their mechanism of action, spectrum, and clinical relevance remain unknown. Methotrexate (MTX), a first-line rheumatoid arthritis (RA) treatment, inhibits mammalian dihydrofolate reductase (DHFR), but whether it directly impacts gut bacteria is unclear. We show that MTX broadly alters the human gut microbiota. Drug sensitivity varied across strains, but the mechanism of action against DHFR appears conserved between mammalian and bacterial cells. RA patient microbiotas were sensitive to MTX, and changes in gut bacterial taxa and gene family abundance were distinct between responders and non-responders. Transplantation of post-treatment samples into germ-free mice given an inflammatory trigger led to reduced immune activation relative to pre-treatment controls, enabling identification of MTX-modulated bacterial taxa associated with intestinal and splenic immune cells. Thus, conservation in cellular pathways across domains of life can result in broad off-target drug effects on the human gut microbiota with consequences for immune function.

Keywords: DMARD; autoimmune disease; human gut microbiome; immune activation; metabolomics; methotrexate; microbiota; off-target effects; purine and pyrimidine biosynthesis; rheumatoid arthritis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arthritis, Rheumatoid / immunology
  • Autoimmune Diseases
  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Bacteria / metabolism*
  • Female
  • Gastrointestinal Microbiome / drug effects*
  • Gastrointestinal Microbiome / immunology
  • Gastrointestinal Tract / immunology*
  • Humans
  • Metabolomics
  • Methotrexate / metabolism*
  • Methotrexate / pharmacology*
  • Mice
  • Mice, Inbred C57BL
  • Phylogeny
  • Purines / metabolism
  • Pyrimidines / metabolism
  • RNA, Ribosomal, 16S / genetics
  • Tetrahydrofolate Dehydrogenase
  • Transcriptome


  • Purines
  • Pyrimidines
  • RNA, Ribosomal, 16S
  • Tetrahydrofolate Dehydrogenase
  • pyrimidine
  • purine
  • Methotrexate